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Two individual chains of microalgae-to-diesel and microalgae-to-butanol were upgraded through process integration and design. According to life cycle assessment (LCA) standards, the two proposed chains were compared in terms of 17 categories of LCA impacts and the sensitivity analysis of LCA impacts on two chains with different lipid or carbohydrate content of microalgae cells was performed. Based on the prescribed specifications and conditions for microalgae cultivation, pretreatment and purity level of the products, LCA analysis revealed that the annual ReCiPe end point score of producing 1 kg biobutanol is lower than that of 1 kg biodiesel by 54.4%. The upgraded microalgae-to-butanol chain could reduce the annual ReCiPe end point score of producing 100 MJ diesel/gasoline from crude oil by 5-10%. The microalgae-to-butanol chain is more ecofriendly than the microalgae-to-diesel chain due to lower LCA impacts such as Climate change human health, Climate change ecosystems, and Fossil depletion.